Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/ed9c5f4040b65650164f2b1a3d25ad/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/ed9c5f4040b65650164f2b1a3d25ad/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/69b1a07291cf51ce7508a88b401932/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)
Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.md.bam --METRICS_FILE BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:23:19.479 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 08:23:19 GMT 2026] MarkDuplicates --INPUT BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.md.bam --METRICS_FILE BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 08:23:19 GMT 2026] Executing as ?@nf-97ed9c5f4040b65650164f2b1a3d25ad-364c9-m9vpw on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-08 08:23:19 MarkDuplicates Start of doWork freeMemory: 105493056; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:23:19 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:23:19 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:23:24 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:6,463,055
INFO 2026-06-08 08:23:24 MarkDuplicates Tracking 3013 as yet unmatched pairs. 61 records in RAM.
INFO 2026-06-08 08:23:26 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: chr1:15,727,695
INFO 2026-06-08 08:23:26 MarkDuplicates Tracking 5693 as yet unmatched pairs. 40 records in RAM.
INFO 2026-06-08 08:23:27 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr1:21,836,825
INFO 2026-06-08 08:23:27 MarkDuplicates Tracking 8440 as yet unmatched pairs. 91 records in RAM.
INFO 2026-06-08 08:23:29 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: chr1:25,811,746
INFO 2026-06-08 08:23:29 MarkDuplicates Tracking 11172 as yet unmatched pairs. 46 records in RAM.
INFO 2026-06-08 08:23:31 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 2s. Last read position: chr1:31,814,061
INFO 2026-06-08 08:23:31 MarkDuplicates Tracking 13839 as yet unmatched pairs. 10 records in RAM.
INFO 2026-06-08 08:23:33 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: chr1:37,943,807
INFO 2026-06-08 08:23:33 MarkDuplicates Tracking 16692 as yet unmatched pairs. 12 records in RAM.
INFO 2026-06-08 08:23:34 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: chr1:43,666,967
INFO 2026-06-08 08:23:34 MarkDuplicates Tracking 19388 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 08:23:36 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: chr1:54,205,054
INFO 2026-06-08 08:23:36 MarkDuplicates Tracking 22182 as yet unmatched pairs. 41 records in RAM.
INFO 2026-06-08 08:23:38 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: chr1:88,887,297
INFO 2026-06-08 08:23:38 MarkDuplicates Tracking 24470 as yet unmatched pairs. 10 records in RAM.
INFO 2026-06-08 08:23:40 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 2s. Last read position: chr1:109,095,727
INFO 2026-06-08 08:23:40 MarkDuplicates Tracking 26770 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 08:23:42 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: chr1:114,730,545
INFO 2026-06-08 08:23:42 MarkDuplicates Tracking 29558 as yet unmatched pairs. 189 records in RAM.
INFO 2026-06-08 08:23:43 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: chr1:119,950,732
INFO 2026-06-08 08:23:43 MarkDuplicates Tracking 31939 as yet unmatched pairs. 263 records in RAM.
INFO 2026-06-08 08:23:45 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: chr1:145,405,187
INFO 2026-06-08 08:23:45 MarkDuplicates Tracking 33381 as yet unmatched pairs. 26 records in RAM.
INFO 2026-06-08 08:23:46 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr1:148,110,512
INFO 2026-06-08 08:23:46 MarkDuplicates Tracking 34845 as yet unmatched pairs. 43 records in RAM.
INFO 2026-06-08 08:23:47 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: chr1:149,535,590
INFO 2026-06-08 08:23:47 MarkDuplicates Tracking 35687 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 08:23:49 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: chr1:150,796,740
INFO 2026-06-08 08:23:49 MarkDuplicates Tracking 38371 as yet unmatched pairs. 235 records in RAM.
INFO 2026-06-08 08:23:51 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: chr1:153,628,422
INFO 2026-06-08 08:23:51 MarkDuplicates Tracking 40761 as yet unmatched pairs. 28 records in RAM.
INFO 2026-06-08 08:23:53 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 1s. Last read position: chr1:154,596,803
INFO 2026-06-08 08:23:53 MarkDuplicates Tracking 43212 as yet unmatched pairs. 244 records in RAM.
INFO 2026-06-08 08:23:54 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 1s. Last read position: chr1:155,190,749
INFO 2026-06-08 08:23:54 MarkDuplicates Tracking 45390 as yet unmatched pairs. 59 records in RAM.
INFO 2026-06-08 08:23:56 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 1s. Last read position: chr1:156,050,308
INFO 2026-06-08 08:23:56 MarkDuplicates Tracking 47574 as yet unmatched pairs. 42 records in RAM.
INFO 2026-06-08 08:23:58 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chr1:158,094,907
INFO 2026-06-08 08:23:58 MarkDuplicates Tracking 50099 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 08:23:59 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr1:161,542,258
INFO 2026-06-08 08:23:59 MarkDuplicates Tracking 52864 as yet unmatched pairs. 277 records in RAM.
INFO 2026-06-08 08:24:01 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr1:168,068,340
INFO 2026-06-08 08:24:01 MarkDuplicates Tracking 54837 as yet unmatched pairs. 123 records in RAM.
INFO 2026-06-08 08:24:03 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 1s. Last read position: chr1:175,160,173
INFO 2026-06-08 08:24:03 MarkDuplicates Tracking 57462 as yet unmatched pairs. 316 records in RAM.
INFO 2026-06-08 08:24:04 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: chr1:183,560,128
INFO 2026-06-08 08:24:04 MarkDuplicates Tracking 59738 as yet unmatched pairs. 52 records in RAM.
INFO 2026-06-08 08:24:06 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 1s. Last read position: chr1:200,842,041
INFO 2026-06-08 08:24:06 MarkDuplicates Tracking 62266 as yet unmatched pairs. 248 records in RAM.
INFO 2026-06-08 08:24:07 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 1s. Last read position: chr1:204,411,318
INFO 2026-06-08 08:24:07 MarkDuplicates Tracking 64758 as yet unmatched pairs. 66 records in RAM.
INFO 2026-06-08 08:24:09 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: chr1:212,807,815
INFO 2026-06-08 08:24:09 MarkDuplicates Tracking 67298 as yet unmatched pairs. 83 records in RAM.
INFO 2026-06-08 08:24:11 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr1:223,627,004
INFO 2026-06-08 08:24:11 MarkDuplicates Tracking 70039 as yet unmatched pairs. 448 records in RAM.
INFO 2026-06-08 08:24:12 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr1:228,106,798
INFO 2026-06-08 08:24:12 MarkDuplicates Tracking 72143 as yet unmatched pairs. 42 records in RAM.
INFO 2026-06-08 08:24:15 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: chr1:234,608,459
INFO 2026-06-08 08:24:15 MarkDuplicates Tracking 75300 as yet unmatched pairs. 218 records in RAM.
INFO 2026-06-08 08:24:17 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: chr1:246,853,219
INFO 2026-06-08 08:24:17 MarkDuplicates Tracking 77725 as yet unmatched pairs. 47 records in RAM.
INFO 2026-06-08 08:24:20 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 3s. Last read position: chr2:20,447,498
INFO 2026-06-08 08:24:20 MarkDuplicates Tracking 80421 as yet unmatched pairs. 80342 records in RAM.
INFO 2026-06-08 08:24:22 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr2:32,388,858
INFO 2026-06-08 08:24:22 MarkDuplicates Tracking 82864 as yet unmatched pairs. 82783 records in RAM.
INFO 2026-06-08 08:24:24 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:24:24 MarkDuplicates Tracking 408482 as yet unmatched pairs. 75929 records in RAM.
INFO 2026-06-08 08:24:26 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:24:26 MarkDuplicates Tracking 709083 as yet unmatched pairs. 69877 records in RAM.
INFO 2026-06-08 08:24:27 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 1s. Last read position: chr2:43,224,889
INFO 2026-06-08 08:24:27 MarkDuplicates Tracking 746982 as yet unmatched pairs. 68008 records in RAM.
INFO 2026-06-08 08:24:29 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr2:55,573,639
INFO 2026-06-08 08:24:29 MarkDuplicates Tracking 744416 as yet unmatched pairs. 65442 records in RAM.
INFO 2026-06-08 08:24:31 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr2:72,961,131
INFO 2026-06-08 08:24:31 MarkDuplicates Tracking 741949 as yet unmatched pairs. 62963 records in RAM.
INFO 2026-06-08 08:24:32 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr2:87,795,744
INFO 2026-06-08 08:24:32 MarkDuplicates Tracking 739496 as yet unmatched pairs. 60510 records in RAM.
INFO 2026-06-08 08:24:34 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr2:99,554,505
INFO 2026-06-08 08:24:34 MarkDuplicates Tracking 737211 as yet unmatched pairs. 58222 records in RAM.
INFO 2026-06-08 08:24:35 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr2:109,836,365
INFO 2026-06-08 08:24:35 MarkDuplicates Tracking 735176 as yet unmatched pairs. 56186 records in RAM.
INFO 2026-06-08 08:24:36 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 1s. Last read position: chr2:127,259,379
INFO 2026-06-08 08:24:36 MarkDuplicates Tracking 733492 as yet unmatched pairs. 54500 records in RAM.
INFO 2026-06-08 08:24:38 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 1s. Last read position: chr2:143,957,318
INFO 2026-06-08 08:24:38 MarkDuplicates Tracking 730970 as yet unmatched pairs. 51977 records in RAM.
INFO 2026-06-08 08:24:40 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr2:151,697,559
INFO 2026-06-08 08:24:40 MarkDuplicates Tracking 729259 as yet unmatched pairs. 50265 records in RAM.
INFO 2026-06-08 08:24:41 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr2:172,498,073
INFO 2026-06-08 08:24:41 MarkDuplicates Tracking 726805 as yet unmatched pairs. 47809 records in RAM.
INFO 2026-06-08 08:24:43 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr2:178,544,284
INFO 2026-06-08 08:24:43 MarkDuplicates Tracking 724734 as yet unmatched pairs. 45738 records in RAM.
INFO 2026-06-08 08:24:45 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr2:178,573,633
INFO 2026-06-08 08:24:45 MarkDuplicates Tracking 722515 as yet unmatched pairs. 43519 records in RAM.
INFO 2026-06-08 08:24:46 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 1s. Last read position: chr2:178,609,658
INFO 2026-06-08 08:24:46 MarkDuplicates Tracking 719981 as yet unmatched pairs. 40985 records in RAM.
INFO 2026-06-08 08:24:48 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: chr2:178,696,108
INFO 2026-06-08 08:24:48 MarkDuplicates Tracking 717784 as yet unmatched pairs. 38788 records in RAM.
INFO 2026-06-08 08:24:50 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr2:178,774,018
INFO 2026-06-08 08:24:50 MarkDuplicates Tracking 715385 as yet unmatched pairs. 36389 records in RAM.
INFO 2026-06-08 08:24:51 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr2:188,990,096
INFO 2026-06-08 08:24:51 MarkDuplicates Tracking 713613 as yet unmatched pairs. 34616 records in RAM.
INFO 2026-06-08 08:24:53 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr2:189,006,206
INFO 2026-06-08 08:24:53 MarkDuplicates Tracking 710194 as yet unmatched pairs. 31197 records in RAM.
INFO 2026-06-08 08:24:55 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr2:190,984,375
INFO 2026-06-08 08:24:55 MarkDuplicates Tracking 706738 as yet unmatched pairs. 27739 records in RAM.
INFO 2026-06-08 08:24:56 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr2:207,567,504
INFO 2026-06-08 08:24:56 MarkDuplicates Tracking 704543 as yet unmatched pairs. 25542 records in RAM.
INFO 2026-06-08 08:24:58 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr2:215,370,307
INFO 2026-06-08 08:24:58 MarkDuplicates Tracking 705748 as yet unmatched pairs. 26747 records in RAM.
INFO 2026-06-08 08:25:01 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: chr2:215,375,636
INFO 2026-06-08 08:25:01 MarkDuplicates Tracking 702205 as yet unmatched pairs. 23203 records in RAM.
INFO 2026-06-08 08:25:03 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 1s. Last read position: chr2:215,384,071
INFO 2026-06-08 08:25:03 MarkDuplicates Tracking 699360 as yet unmatched pairs. 20357 records in RAM.
INFO 2026-06-08 08:25:05 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr2:215,397,719
INFO 2026-06-08 08:25:05 MarkDuplicates Tracking 698045 as yet unmatched pairs. 19042 records in RAM.
INFO 2026-06-08 08:25:06 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 1s. Last read position: chr2:215,409,564
INFO 2026-06-08 08:25:06 MarkDuplicates Tracking 698431 as yet unmatched pairs. 19427 records in RAM.
INFO 2026-06-08 08:25:08 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 1s. Last read position: chr2:215,424,225
INFO 2026-06-08 08:25:08 MarkDuplicates Tracking 692949 as yet unmatched pairs. 13945 records in RAM.
INFO 2026-06-08 08:25:10 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 1s. Last read position: chr2:216,499,347
INFO 2026-06-08 08:25:10 MarkDuplicates Tracking 689033 as yet unmatched pairs. 10013 records in RAM.
INFO 2026-06-08 08:25:11 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 1s. Last read position: chr2:226,796,774
INFO 2026-06-08 08:25:11 MarkDuplicates Tracking 685279 as yet unmatched pairs. 6258 records in RAM.
INFO 2026-06-08 08:25:13 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 1s. Last read position: chr2:237,342,118
INFO 2026-06-08 08:25:13 MarkDuplicates Tracking 682932 as yet unmatched pairs. 3910 records in RAM.
INFO 2026-06-08 08:25:15 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 1s. Last read position: chr2:241,122,757
INFO 2026-06-08 08:25:15 MarkDuplicates Tracking 679976 as yet unmatched pairs. 953 records in RAM.
INFO 2026-06-08 08:25:17 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr3:11,807,862
INFO 2026-06-08 08:25:17 MarkDuplicates Tracking 677257 as yet unmatched pairs. 37621 records in RAM.
INFO 2026-06-08 08:25:18 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 1s. Last read position: chr3:32,764,612
INFO 2026-06-08 08:25:18 MarkDuplicates Tracking 674679 as yet unmatched pairs. 35043 records in RAM.
INFO 2026-06-08 08:25:20 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr3:42,601,107
INFO 2026-06-08 08:25:20 MarkDuplicates Tracking 672142 as yet unmatched pairs. 32502 records in RAM.
INFO 2026-06-08 08:25:21 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr3:48,416,042
INFO 2026-06-08 08:25:21 MarkDuplicates Tracking 669552 as yet unmatched pairs. 29907 records in RAM.
INFO 2026-06-08 08:25:23 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr3:49,531,814
INFO 2026-06-08 08:25:23 MarkDuplicates Tracking 666578 as yet unmatched pairs. 26933 records in RAM.
INFO 2026-06-08 08:25:25 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 1s. Last read position: chr3:52,510,379
INFO 2026-06-08 08:25:25 MarkDuplicates Tracking 664076 as yet unmatched pairs. 24430 records in RAM.
INFO 2026-06-08 08:25:27 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr3:62,203,371
INFO 2026-06-08 08:25:27 MarkDuplicates Tracking 661355 as yet unmatched pairs. 21709 records in RAM.
INFO 2026-06-08 08:25:29 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 2s. Last read position: chr3:101,659,901
INFO 2026-06-08 08:25:29 MarkDuplicates Tracking 658819 as yet unmatched pairs. 19169 records in RAM.
INFO 2026-06-08 08:25:32 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 2s. Last read position: chr3:121,691,812
INFO 2026-06-08 08:25:32 MarkDuplicates Tracking 656534 as yet unmatched pairs. 16883 records in RAM.
INFO 2026-06-08 08:25:33 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr3:128,622,291
INFO 2026-06-08 08:25:33 MarkDuplicates Tracking 653902 as yet unmatched pairs. 14251 records in RAM.
INFO 2026-06-08 08:25:35 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr3:134,550,131
INFO 2026-06-08 08:25:35 MarkDuplicates Tracking 651181 as yet unmatched pairs. 11528 records in RAM.
INFO 2026-06-08 08:25:37 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 1s. Last read position: chr3:150,762,488
INFO 2026-06-08 08:25:37 MarkDuplicates Tracking 648862 as yet unmatched pairs. 9209 records in RAM.
INFO 2026-06-08 08:25:38 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr3:179,210,184
INFO 2026-06-08 08:25:38 MarkDuplicates Tracking 646482 as yet unmatched pairs. 6828 records in RAM.
INFO 2026-06-08 08:25:40 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr3:184,334,727
INFO 2026-06-08 08:25:40 MarkDuplicates Tracking 643936 as yet unmatched pairs. 4282 records in RAM.
INFO 2026-06-08 08:25:41 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr3:195,867,976
INFO 2026-06-08 08:25:41 MarkDuplicates Tracking 641269 as yet unmatched pairs. 1614 records in RAM.
INFO 2026-06-08 08:25:43 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr4:1,737,319
INFO 2026-06-08 08:25:43 MarkDuplicates Tracking 638360 as yet unmatched pairs. 19077 records in RAM.
INFO 2026-06-08 08:25:45 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr4:8,441,424
INFO 2026-06-08 08:25:45 MarkDuplicates Tracking 635139 as yet unmatched pairs. 15855 records in RAM.
INFO 2026-06-08 08:25:46 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 1s. Last read position: chr4:42,018,145
INFO 2026-06-08 08:25:46 MarkDuplicates Tracking 632790 as yet unmatched pairs. 13501 records in RAM.
INFO 2026-06-08 08:25:48 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chr4:75,961,086
INFO 2026-06-08 08:25:48 MarkDuplicates Tracking 630265 as yet unmatched pairs. 10975 records in RAM.
INFO 2026-06-08 08:25:50 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 1s. Last read position: chr4:94,208,489
INFO 2026-06-08 08:25:50 MarkDuplicates Tracking 627754 as yet unmatched pairs. 8460 records in RAM.
INFO 2026-06-08 08:25:51 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 1s. Last read position: chr4:127,885,799
INFO 2026-06-08 08:25:51 MarkDuplicates Tracking 625292 as yet unmatched pairs. 5987 records in RAM.
INFO 2026-06-08 08:25:53 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr4:151,102,868
INFO 2026-06-08 08:25:53 MarkDuplicates Tracking 622994 as yet unmatched pairs. 3686 records in RAM.
INFO 2026-06-08 08:25:54 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 1s. Last read position: chr4:169,731,732
INFO 2026-06-08 08:25:54 MarkDuplicates Tracking 620323 as yet unmatched pairs. 1015 records in RAM.
INFO 2026-06-08 08:25:56 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr5:10,681,095
INFO 2026-06-08 08:25:56 MarkDuplicates Tracking 617730 as yet unmatched pairs. 40314 records in RAM.
INFO 2026-06-08 08:25:58 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr5:34,023,919
INFO 2026-06-08 08:25:58 MarkDuplicates Tracking 615182 as yet unmatched pairs. 37760 records in RAM.
INFO 2026-06-08 08:25:59 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 1s. Last read position: chr5:55,110,037
INFO 2026-06-08 08:25:59 MarkDuplicates Tracking 612790 as yet unmatched pairs. 35368 records in RAM.
INFO 2026-06-08 08:26:02 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 2s. Last read position: chr5:69,568,197
INFO 2026-06-08 08:26:02 MarkDuplicates Tracking 610991 as yet unmatched pairs. 33569 records in RAM.
INFO 2026-06-08 08:26:03 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr5:72,193,958
INFO 2026-06-08 08:26:03 MarkDuplicates Tracking 609375 as yet unmatched pairs. 31953 records in RAM.
INFO 2026-06-08 08:26:05 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr5:83,538,876
INFO 2026-06-08 08:26:05 MarkDuplicates Tracking 606897 as yet unmatched pairs. 29474 records in RAM.
INFO 2026-06-08 08:26:07 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: chr5:110,743,773
INFO 2026-06-08 08:26:07 MarkDuplicates Tracking 604752 as yet unmatched pairs. 27328 records in RAM.
INFO 2026-06-08 08:26:09 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr5:132,897,043
INFO 2026-06-08 08:26:09 MarkDuplicates Tracking 602221 as yet unmatched pairs. 24797 records in RAM.
INFO 2026-06-08 08:26:11 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr5:135,571,227
INFO 2026-06-08 08:26:11 MarkDuplicates Tracking 604871 as yet unmatched pairs. 27433 records in RAM.
INFO 2026-06-08 08:26:13 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 1s. Last read position: chr5:138,399,942
INFO 2026-06-08 08:26:13 MarkDuplicates Tracking 596617 as yet unmatched pairs. 19178 records in RAM.
INFO 2026-06-08 08:26:14 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr5:141,210,561
INFO 2026-06-08 08:26:14 MarkDuplicates Tracking 594094 as yet unmatched pairs. 16637 records in RAM.
INFO 2026-06-08 08:26:16 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr5:150,117,650
INFO 2026-06-08 08:26:16 MarkDuplicates Tracking 591727 as yet unmatched pairs. 14269 records in RAM.
INFO 2026-06-08 08:26:17 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr5:150,405,098
INFO 2026-06-08 08:26:17 MarkDuplicates Tracking 591428 as yet unmatched pairs. 13970 records in RAM.
INFO 2026-06-08 08:26:19 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr5:151,667,521
INFO 2026-06-08 08:26:19 MarkDuplicates Tracking 586064 as yet unmatched pairs. 8605 records in RAM.
INFO 2026-06-08 08:26:21 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr5:171,400,199
INFO 2026-06-08 08:26:21 MarkDuplicates Tracking 583864 as yet unmatched pairs. 6402 records in RAM.
INFO 2026-06-08 08:26:22 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 1s. Last read position: chr5:178,149,767
INFO 2026-06-08 08:26:22 MarkDuplicates Tracking 580690 as yet unmatched pairs. 3226 records in RAM.
INFO 2026-06-08 08:26:24 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr5:180,791,853
INFO 2026-06-08 08:26:24 MarkDuplicates Tracking 578191 as yet unmatched pairs. 727 records in RAM.
INFO 2026-06-08 08:26:26 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 2s. Last read position: chr6:13,584,143
INFO 2026-06-08 08:26:26 MarkDuplicates Tracking 575329 as yet unmatched pairs. 33048 records in RAM.
INFO 2026-06-08 08:26:28 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 1s. Last read position: chr6:27,824,243
INFO 2026-06-08 08:26:28 MarkDuplicates Tracking 572733 as yet unmatched pairs. 30452 records in RAM.
INFO 2026-06-08 08:26:29 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr6:31,270,260
INFO 2026-06-08 08:26:29 MarkDuplicates Tracking 570536 as yet unmatched pairs. 28255 records in RAM.
INFO 2026-06-08 08:26:31 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr6:31,816,377
INFO 2026-06-08 08:26:31 MarkDuplicates Tracking 567834 as yet unmatched pairs. 25551 records in RAM.
INFO 2026-06-08 08:26:32 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr6:31,992,211
INFO 2026-06-08 08:26:32 MarkDuplicates Tracking 566014 as yet unmatched pairs. 23730 records in RAM.
INFO 2026-06-08 08:26:34 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr6:32,554,751
INFO 2026-06-08 08:26:34 MarkDuplicates Tracking 563960 as yet unmatched pairs. 21676 records in RAM.
INFO 2026-06-08 08:26:37 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 3s. Last read position: chr6:33,417,284
INFO 2026-06-08 08:26:37 MarkDuplicates Tracking 560967 as yet unmatched pairs. 18683 records in RAM.
INFO 2026-06-08 08:26:39 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: chr6:42,658,765
INFO 2026-06-08 08:26:39 MarkDuplicates Tracking 558324 as yet unmatched pairs. 16040 records in RAM.
INFO 2026-06-08 08:26:40 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr6:53,920,672
INFO 2026-06-08 08:26:40 MarkDuplicates Tracking 555716 as yet unmatched pairs. 13432 records in RAM.
INFO 2026-06-08 08:26:42 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr6:75,202,723
INFO 2026-06-08 08:26:42 MarkDuplicates Tracking 553631 as yet unmatched pairs. 11346 records in RAM.
INFO 2026-06-08 08:26:43 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr6:109,368,864
INFO 2026-06-08 08:26:43 MarkDuplicates Tracking 551429 as yet unmatched pairs. 9131 records in RAM.
INFO 2026-06-08 08:26:45 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 1s. Last read position: chr6:136,346,044
INFO 2026-06-08 08:26:45 MarkDuplicates Tracking 548261 as yet unmatched pairs. 5962 records in RAM.
INFO 2026-06-08 08:26:47 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr6:152,011,620
INFO 2026-06-08 08:26:47 MarkDuplicates Tracking 546508 as yet unmatched pairs. 4209 records in RAM.
INFO 2026-06-08 08:26:48 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr6:163,570,688
INFO 2026-06-08 08:26:48 MarkDuplicates Tracking 543374 as yet unmatched pairs. 1072 records in RAM.
INFO 2026-06-08 08:26:51 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 2s. Last read position: chr7:5,345,748
INFO 2026-06-08 08:26:51 MarkDuplicates Tracking 540393 as yet unmatched pairs. 35069 records in RAM.
INFO 2026-06-08 08:26:53 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 1s. Last read position: chr7:5,912,860
INFO 2026-06-08 08:26:53 MarkDuplicates Tracking 537664 as yet unmatched pairs. 32339 records in RAM.
INFO 2026-06-08 08:26:55 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr7:27,840,654
INFO 2026-06-08 08:26:55 MarkDuplicates Tracking 535220 as yet unmatched pairs. 29894 records in RAM.
INFO 2026-06-08 08:26:56 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr7:44,565,967
INFO 2026-06-08 08:26:56 MarkDuplicates Tracking 532841 as yet unmatched pairs. 27513 records in RAM.
INFO 2026-06-08 08:26:58 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr7:72,954,355
INFO 2026-06-08 08:26:58 MarkDuplicates Tracking 530425 as yet unmatched pairs. 25094 records in RAM.
INFO 2026-06-08 08:26:59 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr7:76,003,795
INFO 2026-06-08 08:26:59 MarkDuplicates Tracking 528717 as yet unmatched pairs. 23385 records in RAM.
INFO 2026-06-08 08:27:01 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 2s. Last read position: chr7:92,002,645
INFO 2026-06-08 08:27:01 MarkDuplicates Tracking 526223 as yet unmatched pairs. 20890 records in RAM.
INFO 2026-06-08 08:27:04 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 2s. Last read position: chr7:94,408,197
INFO 2026-06-08 08:27:04 MarkDuplicates Tracking 525244 as yet unmatched pairs. 19911 records in RAM.
INFO 2026-06-08 08:27:06 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr7:94,427,009
INFO 2026-06-08 08:27:06 MarkDuplicates Tracking 521168 as yet unmatched pairs. 15835 records in RAM.
INFO 2026-06-08 08:27:07 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr7:100,153,501
INFO 2026-06-08 08:27:07 MarkDuplicates Tracking 517836 as yet unmatched pairs. 12500 records in RAM.
INFO 2026-06-08 08:27:09 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 1s. Last read position: chr7:102,553,291
INFO 2026-06-08 08:27:09 MarkDuplicates Tracking 515914 as yet unmatched pairs. 10577 records in RAM.
INFO 2026-06-08 08:27:11 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr7:111,872,051
INFO 2026-06-08 08:27:11 MarkDuplicates Tracking 513791 as yet unmatched pairs. 8454 records in RAM.
INFO 2026-06-08 08:27:13 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 2s. Last read position: chr7:133,317,351
INFO 2026-06-08 08:27:13 MarkDuplicates Tracking 511265 as yet unmatched pairs. 5928 records in RAM.
INFO 2026-06-08 08:27:15 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 2s. Last read position: chr7:143,572,401
INFO 2026-06-08 08:27:15 MarkDuplicates Tracking 508612 as yet unmatched pairs. 3273 records in RAM.
INFO 2026-06-08 08:27:17 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr7:152,148,863
INFO 2026-06-08 08:27:17 MarkDuplicates Tracking 506416 as yet unmatched pairs. 1077 records in RAM.
INFO 2026-06-08 08:27:19 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr8:17,560,369
INFO 2026-06-08 08:27:19 MarkDuplicates Tracking 503988 as yet unmatched pairs. 27576 records in RAM.
INFO 2026-06-08 08:27:20 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 1s. Last read position: chr8:37,696,175
INFO 2026-06-08 08:27:20 MarkDuplicates Tracking 501199 as yet unmatched pairs. 24786 records in RAM.
INFO 2026-06-08 08:27:22 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr8:42,765,178
INFO 2026-06-08 08:27:22 MarkDuplicates Tracking 498636 as yet unmatched pairs. 22223 records in RAM.
INFO 2026-06-08 08:27:24 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr8:66,665,824
INFO 2026-06-08 08:27:24 MarkDuplicates Tracking 496038 as yet unmatched pairs. 19625 records in RAM.
INFO 2026-06-08 08:27:25 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr8:86,461,826
INFO 2026-06-08 08:27:25 MarkDuplicates Tracking 493722 as yet unmatched pairs. 17308 records in RAM.
INFO 2026-06-08 08:27:27 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 1s. Last read position: chr8:100,721,396
INFO 2026-06-08 08:27:27 MarkDuplicates Tracking 491234 as yet unmatched pairs. 14820 records in RAM.
INFO 2026-06-08 08:27:29 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 2s. Last read position: chr8:115,604,986
INFO 2026-06-08 08:27:29 MarkDuplicates Tracking 489340 as yet unmatched pairs. 12924 records in RAM.
INFO 2026-06-08 08:27:32 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 2s. Last read position: chr8:133,044,999
INFO 2026-06-08 08:27:32 MarkDuplicates Tracking 486248 as yet unmatched pairs. 9831 records in RAM.
INFO 2026-06-08 08:27:33 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr8:143,858,367
INFO 2026-06-08 08:27:33 MarkDuplicates Tracking 483263 as yet unmatched pairs. 6845 records in RAM.
INFO 2026-06-08 08:27:34 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,390
INFO 2026-06-08 08:27:34 MarkDuplicates Tracking 482167 as yet unmatched pairs. 5746 records in RAM.
INFO 2026-06-08 08:27:36 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr8:143,921,313
INFO 2026-06-08 08:27:36 MarkDuplicates Tracking 480904 as yet unmatched pairs. 4483 records in RAM.
INFO 2026-06-08 08:27:37 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr8:144,497,286
INFO 2026-06-08 08:27:37 MarkDuplicates Tracking 477247 as yet unmatched pairs. 825 records in RAM.
INFO 2026-06-08 08:27:39 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr9:20,770,084
INFO 2026-06-08 08:27:39 MarkDuplicates Tracking 474874 as yet unmatched pairs. 24008 records in RAM.
INFO 2026-06-08 08:27:42 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 2s. Last read position: chr9:35,724,643
INFO 2026-06-08 08:27:42 MarkDuplicates Tracking 472338 as yet unmatched pairs. 21469 records in RAM.
INFO 2026-06-08 08:27:43 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr9:85,632,757
INFO 2026-06-08 08:27:43 MarkDuplicates Tracking 470211 as yet unmatched pairs. 19337 records in RAM.
INFO 2026-06-08 08:27:45 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 1s. Last read position: chr9:99,035,368
INFO 2026-06-08 08:27:45 MarkDuplicates Tracking 467418 as yet unmatched pairs. 16541 records in RAM.
INFO 2026-06-08 08:27:47 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr9:115,024,042
INFO 2026-06-08 08:27:47 MarkDuplicates Tracking 464731 as yet unmatched pairs. 13854 records in RAM.
INFO 2026-06-08 08:27:48 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 1s. Last read position: chr9:125,543,143
INFO 2026-06-08 08:27:48 MarkDuplicates Tracking 462078 as yet unmatched pairs. 11200 records in RAM.
INFO 2026-06-08 08:27:50 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr9:129,097,252
INFO 2026-06-08 08:27:50 MarkDuplicates Tracking 459115 as yet unmatched pairs. 8237 records in RAM.
INFO 2026-06-08 08:27:52 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 2s. Last read position: chr9:134,033,552
INFO 2026-06-08 08:27:52 MarkDuplicates Tracking 456586 as yet unmatched pairs. 5704 records in RAM.
INFO 2026-06-08 08:27:53 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 1s. Last read position: chr9:136,925,838
INFO 2026-06-08 08:27:53 MarkDuplicates Tracking 453203 as yet unmatched pairs. 2317 records in RAM.
INFO 2026-06-08 08:27:55 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr10:5,742,286
INFO 2026-06-08 08:27:55 MarkDuplicates Tracking 450101 as yet unmatched pairs. 22783 records in RAM.
INFO 2026-06-08 08:27:57 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 2s. Last read position: chr10:24,533,096
INFO 2026-06-08 08:27:57 MarkDuplicates Tracking 447531 as yet unmatched pairs. 20211 records in RAM.
INFO 2026-06-08 08:28:00 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 2s. Last read position: chr10:35,032,436
INFO 2026-06-08 08:28:00 MarkDuplicates Tracking 445398 as yet unmatched pairs. 18077 records in RAM.
INFO 2026-06-08 08:28:02 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr10:45,777,404
INFO 2026-06-08 08:28:02 MarkDuplicates Tracking 442450 as yet unmatched pairs. 15128 records in RAM.
INFO 2026-06-08 08:28:03 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: chr10:69,015,814
INFO 2026-06-08 08:28:03 MarkDuplicates Tracking 440455 as yet unmatched pairs. 13133 records in RAM.
INFO 2026-06-08 08:28:05 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr10:78,035,539
INFO 2026-06-08 08:28:05 MarkDuplicates Tracking 438464 as yet unmatched pairs. 11140 records in RAM.
INFO 2026-06-08 08:28:06 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr10:92,470,280
INFO 2026-06-08 08:28:06 MarkDuplicates Tracking 435588 as yet unmatched pairs. 8264 records in RAM.
INFO 2026-06-08 08:28:08 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 1s. Last read position: chr10:101,799,383
INFO 2026-06-08 08:28:08 MarkDuplicates Tracking 433034 as yet unmatched pairs. 5708 records in RAM.
INFO 2026-06-08 08:28:09 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr10:116,979,262
INFO 2026-06-08 08:28:09 MarkDuplicates Tracking 430517 as yet unmatched pairs. 3189 records in RAM.
INFO 2026-06-08 08:28:11 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 1s. Last read position: chr10:132,405,435
INFO 2026-06-08 08:28:11 MarkDuplicates Tracking 427789 as yet unmatched pairs. 460 records in RAM.
INFO 2026-06-08 08:28:13 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 2s. Last read position: chr11:419,642
INFO 2026-06-08 08:28:13 MarkDuplicates Tracking 424703 as yet unmatched pairs. 46486 records in RAM.
INFO 2026-06-08 08:28:15 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 1s. Last read position: chr11:3,126,500
INFO 2026-06-08 08:28:15 MarkDuplicates Tracking 421640 as yet unmatched pairs. 43421 records in RAM.
INFO 2026-06-08 08:28:16 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 1s. Last read position: chr11:10,799,646
INFO 2026-06-08 08:28:16 MarkDuplicates Tracking 419780 as yet unmatched pairs. 41561 records in RAM.
INFO 2026-06-08 08:28:18 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 1s. Last read position: chr11:33,287,123
INFO 2026-06-08 08:28:18 MarkDuplicates Tracking 416737 as yet unmatched pairs. 38517 records in RAM.
INFO 2026-06-08 08:28:20 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr11:47,175,084
INFO 2026-06-08 08:28:20 MarkDuplicates Tracking 413946 as yet unmatched pairs. 35726 records in RAM.
INFO 2026-06-08 08:28:22 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 2s. Last read position: chr11:60,900,589
INFO 2026-06-08 08:28:22 MarkDuplicates Tracking 411211 as yet unmatched pairs. 32989 records in RAM.
INFO 2026-06-08 08:28:24 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 1s. Last read position: chr11:62,517,276
INFO 2026-06-08 08:28:24 MarkDuplicates Tracking 409722 as yet unmatched pairs. 31498 records in RAM.
INFO 2026-06-08 08:28:26 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr11:62,527,628
INFO 2026-06-08 08:28:26 MarkDuplicates Tracking 407130 as yet unmatched pairs. 28906 records in RAM.
INFO 2026-06-08 08:28:27 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 1s. Last read position: chr11:62,663,064
INFO 2026-06-08 08:28:27 MarkDuplicates Tracking 404176 as yet unmatched pairs. 25950 records in RAM.
INFO 2026-06-08 08:28:29 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 1s. Last read position: chr11:65,120,761
INFO 2026-06-08 08:28:29 MarkDuplicates Tracking 401342 as yet unmatched pairs. 23116 records in RAM.
INFO 2026-06-08 08:28:31 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr11:66,437,213
INFO 2026-06-08 08:28:31 MarkDuplicates Tracking 397969 as yet unmatched pairs. 19742 records in RAM.
INFO 2026-06-08 08:28:32 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr11:70,149,745
INFO 2026-06-08 08:28:32 MarkDuplicates Tracking 394929 as yet unmatched pairs. 16702 records in RAM.
INFO 2026-06-08 08:28:34 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr11:72,822,522
INFO 2026-06-08 08:28:34 MarkDuplicates Tracking 392066 as yet unmatched pairs. 13839 records in RAM.
INFO 2026-06-08 08:28:36 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 2s. Last read position: chr11:76,065,711
INFO 2026-06-08 08:28:36 MarkDuplicates Tracking 389377 as yet unmatched pairs. 11150 records in RAM.
INFO 2026-06-08 08:28:39 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 2s. Last read position: chr11:78,079,658
INFO 2026-06-08 08:28:39 MarkDuplicates Tracking 387292 as yet unmatched pairs. 9065 records in RAM.
INFO 2026-06-08 08:28:40 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr11:96,341,426
INFO 2026-06-08 08:28:40 MarkDuplicates Tracking 384435 as yet unmatched pairs. 6207 records in RAM.
INFO 2026-06-08 08:28:42 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr11:118,535,524
INFO 2026-06-08 08:28:42 MarkDuplicates Tracking 381860 as yet unmatched pairs. 3632 records in RAM.
INFO 2026-06-08 08:28:44 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr11:125,613,116
INFO 2026-06-08 08:28:44 MarkDuplicates Tracking 379476 as yet unmatched pairs. 1248 records in RAM.
INFO 2026-06-08 08:28:46 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 2s. Last read position: chr12:2,803,157
INFO 2026-06-08 08:28:46 MarkDuplicates Tracking 377356 as yet unmatched pairs. 52231 records in RAM.
INFO 2026-06-08 08:28:48 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 2s. Last read position: chr12:6,869,358
INFO 2026-06-08 08:28:48 MarkDuplicates Tracking 374516 as yet unmatched pairs. 49390 records in RAM.
INFO 2026-06-08 08:28:50 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 2s. Last read position: chr12:12,908,478
INFO 2026-06-08 08:28:50 MarkDuplicates Tracking 372401 as yet unmatched pairs. 47274 records in RAM.
INFO 2026-06-08 08:28:52 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chr12:30,690,500
INFO 2026-06-08 08:28:52 MarkDuplicates Tracking 369422 as yet unmatched pairs. 44293 records in RAM.
INFO 2026-06-08 08:28:54 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 1s. Last read position: chr12:40,481,437
INFO 2026-06-08 08:28:54 MarkDuplicates Tracking 367240 as yet unmatched pairs. 42110 records in RAM.
INFO 2026-06-08 08:28:55 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr12:40,487,388
INFO 2026-06-08 08:28:55 MarkDuplicates Tracking 366059 as yet unmatched pairs. 40927 records in RAM.
INFO 2026-06-08 08:28:57 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr12:40,499,697
INFO 2026-06-08 08:28:57 MarkDuplicates Tracking 361421 as yet unmatched pairs. 36280 records in RAM.
INFO 2026-06-08 08:28:58 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr12:42,313,105
INFO 2026-06-08 08:28:58 MarkDuplicates Tracking 359351 as yet unmatched pairs. 34210 records in RAM.
INFO 2026-06-08 08:29:00 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr12:49,040,276
INFO 2026-06-08 08:29:00 MarkDuplicates Tracking 357045 as yet unmatched pairs. 31902 records in RAM.
INFO 2026-06-08 08:29:02 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr12:50,813,837
INFO 2026-06-08 08:29:02 MarkDuplicates Tracking 354621 as yet unmatched pairs. 29477 records in RAM.
INFO 2026-06-08 08:29:03 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr12:53,467,221
INFO 2026-06-08 08:29:03 MarkDuplicates Tracking 352544 as yet unmatched pairs. 27398 records in RAM.
INFO 2026-06-08 08:29:05 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 2s. Last read position: chr12:56,138,373
INFO 2026-06-08 08:29:05 MarkDuplicates Tracking 349425 as yet unmatched pairs. 24278 records in RAM.
INFO 2026-06-08 08:29:08 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 2s. Last read position: chr12:56,746,044
INFO 2026-06-08 08:29:08 MarkDuplicates Tracking 347031 as yet unmatched pairs. 21883 records in RAM.
INFO 2026-06-08 08:29:09 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 1s. Last read position: chr12:57,532,980
INFO 2026-06-08 08:29:09 MarkDuplicates Tracking 344113 as yet unmatched pairs. 18964 records in RAM.
INFO 2026-06-08 08:29:11 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr12:71,627,789
INFO 2026-06-08 08:29:11 MarkDuplicates Tracking 341560 as yet unmatched pairs. 16411 records in RAM.
INFO 2026-06-08 08:29:12 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chr12:98,531,822
INFO 2026-06-08 08:29:12 MarkDuplicates Tracking 339284 as yet unmatched pairs. 14134 records in RAM.
INFO 2026-06-08 08:29:14 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chr12:106,977,896
INFO 2026-06-08 08:29:14 MarkDuplicates Tracking 336799 as yet unmatched pairs. 11649 records in RAM.
INFO 2026-06-08 08:29:15 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chr12:112,405,254
INFO 2026-06-08 08:29:15 MarkDuplicates Tracking 334694 as yet unmatched pairs. 9544 records in RAM.
INFO 2026-06-08 08:29:17 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 1s. Last read position: chr12:120,173,806
INFO 2026-06-08 08:29:17 MarkDuplicates Tracking 331680 as yet unmatched pairs. 6530 records in RAM.
INFO 2026-06-08 08:29:19 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 2s. Last read position: chr12:123,320,465
INFO 2026-06-08 08:29:19 MarkDuplicates Tracking 328760 as yet unmatched pairs. 3609 records in RAM.
INFO 2026-06-08 08:29:21 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 1s. Last read position: chr12:132,718,087
INFO 2026-06-08 08:29:21 MarkDuplicates Tracking 325886 as yet unmatched pairs. 734 records in RAM.
INFO 2026-06-08 08:29:23 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 2s. Last read position: chr13:32,699,772
INFO 2026-06-08 08:29:23 MarkDuplicates Tracking 323371 as yet unmatched pairs. 6803 records in RAM.
INFO 2026-06-08 08:29:25 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 2s. Last read position: chr13:49,207,113
INFO 2026-06-08 08:29:25 MarkDuplicates Tracking 321020 as yet unmatched pairs. 4452 records in RAM.
INFO 2026-06-08 08:29:26 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 1s. Last read position: chr13:102,616,434
INFO 2026-06-08 08:29:26 MarkDuplicates Tracking 318557 as yet unmatched pairs. 1987 records in RAM.
INFO 2026-06-08 08:29:28 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 1s. Last read position: chr14:21,084,798
INFO 2026-06-08 08:29:28 MarkDuplicates Tracking 315908 as yet unmatched pairs. 24409 records in RAM.
INFO 2026-06-08 08:29:30 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 1s. Last read position: chr14:24,120,901
INFO 2026-06-08 08:29:30 MarkDuplicates Tracking 313488 as yet unmatched pairs. 21988 records in RAM.
INFO 2026-06-08 08:29:31 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: chr14:35,308,079
INFO 2026-06-08 08:29:31 MarkDuplicates Tracking 310946 as yet unmatched pairs. 19444 records in RAM.
INFO 2026-06-08 08:29:33 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 1s. Last read position: chr14:52,778,327
INFO 2026-06-08 08:29:33 MarkDuplicates Tracking 308421 as yet unmatched pairs. 16919 records in RAM.
INFO 2026-06-08 08:29:34 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr14:64,388,405
INFO 2026-06-08 08:29:34 MarkDuplicates Tracking 305854 as yet unmatched pairs. 14351 records in RAM.
INFO 2026-06-08 08:29:37 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 2s. Last read position: chr14:73,277,122
INFO 2026-06-08 08:29:37 MarkDuplicates Tracking 303465 as yet unmatched pairs. 11962 records in RAM.
INFO 2026-06-08 08:29:38 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr14:88,596,746
INFO 2026-06-08 08:29:38 MarkDuplicates Tracking 300663 as yet unmatched pairs. 9159 records in RAM.
INFO 2026-06-08 08:29:40 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 1s. Last read position: chr14:95,455,695
INFO 2026-06-08 08:29:40 MarkDuplicates Tracking 298018 as yet unmatched pairs. 6513 records in RAM.
INFO 2026-06-08 08:29:41 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr14:102,085,898
INFO 2026-06-08 08:29:41 MarkDuplicates Tracking 295491 as yet unmatched pairs. 3984 records in RAM.
INFO 2026-06-08 08:29:42 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 1s. Last read position: chr14:105,384,937
INFO 2026-06-08 08:29:42 MarkDuplicates Tracking 292493 as yet unmatched pairs. 985 records in RAM.
INFO 2026-06-08 08:29:44 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 1s. Last read position: chr15:29,268,743
INFO 2026-06-08 08:29:44 MarkDuplicates Tracking 290311 as yet unmatched pairs. 17542 records in RAM.
INFO 2026-06-08 08:29:46 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 1s. Last read position: chr15:40,776,555
INFO 2026-06-08 08:29:46 MarkDuplicates Tracking 287811 as yet unmatched pairs. 15042 records in RAM.
INFO 2026-06-08 08:29:47 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 1s. Last read position: chr15:43,793,755
INFO 2026-06-08 08:29:47 MarkDuplicates Tracking 286218 as yet unmatched pairs. 13449 records in RAM.
INFO 2026-06-08 08:29:49 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 1s. Last read position: chr15:55,182,090
INFO 2026-06-08 08:29:49 MarkDuplicates Tracking 282791 as yet unmatched pairs. 10021 records in RAM.
INFO 2026-06-08 08:29:51 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 2s. Last read position: chr15:64,748,506
INFO 2026-06-08 08:29:51 MarkDuplicates Tracking 280284 as yet unmatched pairs. 7513 records in RAM.
INFO 2026-06-08 08:29:53 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr15:74,035,126
INFO 2026-06-08 08:29:53 MarkDuplicates Tracking 277692 as yet unmatched pairs. 4919 records in RAM.
INFO 2026-06-08 08:29:54 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 1s. Last read position: chr15:85,245,239
INFO 2026-06-08 08:29:54 MarkDuplicates Tracking 275050 as yet unmatched pairs. 2277 records in RAM.
INFO 2026-06-08 08:29:56 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 1s. Last read position: chr16:189,176
INFO 2026-06-08 08:29:56 MarkDuplicates Tracking 272619 as yet unmatched pairs. 42905 records in RAM.
INFO 2026-06-08 08:29:58 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 1s. Last read position: chr16:1,223,372
INFO 2026-06-08 08:29:58 MarkDuplicates Tracking 269025 as yet unmatched pairs. 39311 records in RAM.
INFO 2026-06-08 08:29:59 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 1s. Last read position: chr16:2,108,786
INFO 2026-06-08 08:29:59 MarkDuplicates Tracking 265641 as yet unmatched pairs. 35927 records in RAM.
INFO 2026-06-08 08:30:00 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 1s. Last read position: chr16:2,769,160
INFO 2026-06-08 08:30:00 MarkDuplicates Tracking 263064 as yet unmatched pairs. 33350 records in RAM.
INFO 2026-06-08 08:30:02 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 1s. Last read position: chr16:4,795,955
INFO 2026-06-08 08:30:02 MarkDuplicates Tracking 260602 as yet unmatched pairs. 30888 records in RAM.
INFO 2026-06-08 08:30:03 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 1s. Last read position: chr16:14,627,305
INFO 2026-06-08 08:30:03 MarkDuplicates Tracking 257837 as yet unmatched pairs. 28122 records in RAM.
INFO 2026-06-08 08:30:05 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 1s. Last read position: chr16:15,135,578
INFO 2026-06-08 08:30:05 MarkDuplicates Tracking 256520 as yet unmatched pairs. 26805 records in RAM.
INFO 2026-06-08 08:30:06 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 1s. Last read position: chr16:16,358,510
INFO 2026-06-08 08:30:06 MarkDuplicates Tracking 255637 as yet unmatched pairs. 25922 records in RAM.
INFO 2026-06-08 08:30:07 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 1s. Last read position: chr16:18,380,657
INFO 2026-06-08 08:30:07 MarkDuplicates Tracking 254737 as yet unmatched pairs. 25021 records in RAM.
INFO 2026-06-08 08:30:08 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 1s. Last read position: chr16:19,536,221
INFO 2026-06-08 08:30:08 MarkDuplicates Tracking 252715 as yet unmatched pairs. 22997 records in RAM.
INFO 2026-06-08 08:30:10 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 1s. Last read position: chr16:21,887,986
INFO 2026-06-08 08:30:10 MarkDuplicates Tracking 251691 as yet unmatched pairs. 21973 records in RAM.
INFO 2026-06-08 08:30:11 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 1s. Last read position: chr16:24,823,572
INFO 2026-06-08 08:30:11 MarkDuplicates Tracking 250280 as yet unmatched pairs. 20562 records in RAM.
INFO 2026-06-08 08:30:13 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 1s. Last read position: chr16:29,382,133
INFO 2026-06-08 08:30:13 MarkDuplicates Tracking 248055 as yet unmatched pairs. 18337 records in RAM.
INFO 2026-06-08 08:30:14 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 1s. Last read position: chr16:29,996,547
INFO 2026-06-08 08:30:14 MarkDuplicates Tracking 246167 as yet unmatched pairs. 16449 records in RAM.
INFO 2026-06-08 08:30:16 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 1s. Last read position: chr16:30,704,207
INFO 2026-06-08 08:30:16 MarkDuplicates Tracking 244083 as yet unmatched pairs. 14365 records in RAM.
INFO 2026-06-08 08:30:18 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 1s. Last read position: chr16:32,174,324
INFO 2026-06-08 08:30:18 MarkDuplicates Tracking 241189 as yet unmatched pairs. 11470 records in RAM.
INFO 2026-06-08 08:30:19 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 1s. Last read position: chr16:58,040,688
INFO 2026-06-08 08:30:19 MarkDuplicates Tracking 238463 as yet unmatched pairs. 8742 records in RAM.
INFO 2026-06-08 08:30:21 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 1s. Last read position: chr16:69,711,105
INFO 2026-06-08 08:30:21 MarkDuplicates Tracking 235670 as yet unmatched pairs. 5948 records in RAM.
INFO 2026-06-08 08:30:22 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 1s. Last read position: chr16:84,180,227
INFO 2026-06-08 08:30:22 MarkDuplicates Tracking 233169 as yet unmatched pairs. 3447 records in RAM.
INFO 2026-06-08 08:30:23 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 1s. Last read position: chr16:89,907,257
INFO 2026-06-08 08:30:23 MarkDuplicates Tracking 230028 as yet unmatched pairs. 305 records in RAM.
INFO 2026-06-08 08:30:25 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 2s. Last read position: chr17:4,718,664
INFO 2026-06-08 08:30:25 MarkDuplicates Tracking 227145 as yet unmatched pairs. 95011 records in RAM.
INFO 2026-06-08 08:30:27 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 1s. Last read position: chr17:7,559,042
INFO 2026-06-08 08:30:27 MarkDuplicates Tracking 224407 as yet unmatched pairs. 92272 records in RAM.
INFO 2026-06-08 08:30:28 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 1s. Last read position: chr17:16,101,365
INFO 2026-06-08 08:30:28 MarkDuplicates Tracking 222120 as yet unmatched pairs. 89985 records in RAM.
INFO 2026-06-08 08:30:30 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 1s. Last read position: chr17:28,618,940
INFO 2026-06-08 08:30:30 MarkDuplicates Tracking 219557 as yet unmatched pairs. 87422 records in RAM.
INFO 2026-06-08 08:30:31 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 1s. Last read position: chr17:31,937,466
INFO 2026-06-08 08:30:31 MarkDuplicates Tracking 216910 as yet unmatched pairs. 84774 records in RAM.
INFO 2026-06-08 08:30:33 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 1s. Last read position: chr17:37,538,355
INFO 2026-06-08 08:30:33 MarkDuplicates Tracking 214617 as yet unmatched pairs. 82481 records in RAM.
INFO 2026-06-08 08:30:34 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 1s. Last read position: chr17:39,526,297
INFO 2026-06-08 08:30:34 MarkDuplicates Tracking 212469 as yet unmatched pairs. 80333 records in RAM.
INFO 2026-06-08 08:30:36 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 1s. Last read position: chr17:39,719,804
INFO 2026-06-08 08:30:36 MarkDuplicates Tracking 211979 as yet unmatched pairs. 79843 records in RAM.
INFO 2026-06-08 08:30:37 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 1s. Last read position: chr17:40,291,502
INFO 2026-06-08 08:30:37 MarkDuplicates Tracking 206858 as yet unmatched pairs. 74722 records in RAM.
INFO 2026-06-08 08:30:39 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 1s. Last read position: chr17:41,835,865
INFO 2026-06-08 08:30:39 MarkDuplicates Tracking 203734 as yet unmatched pairs. 71598 records in RAM.
INFO 2026-06-08 08:31:40 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 61s. Last read position: chr17:43,016,508
INFO 2026-06-08 08:31:40 MarkDuplicates Tracking 200828 as yet unmatched pairs. 68692 records in RAM.
INFO 2026-06-08 08:31:41 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 1s. Last read position: chr17:45,475,642
INFO 2026-06-08 08:31:41 MarkDuplicates Tracking 197848 as yet unmatched pairs. 65712 records in RAM.
INFO 2026-06-08 08:31:43 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 1s. Last read position: chr17:49,298,434
INFO 2026-06-08 08:31:43 MarkDuplicates Tracking 196070 as yet unmatched pairs. 63933 records in RAM.
INFO 2026-06-08 08:31:46 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 2s. Last read position: chr17:50,186,410
INFO 2026-06-08 08:31:46 MarkDuplicates Tracking 195546 as yet unmatched pairs. 63409 records in RAM.
INFO 2026-06-08 08:31:47 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,483
INFO 2026-06-08 08:31:47 MarkDuplicates Tracking 198066 as yet unmatched pairs. 65928 records in RAM.
INFO 2026-06-08 08:31:49 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,560
INFO 2026-06-08 08:31:49 MarkDuplicates Tracking 195701 as yet unmatched pairs. 63563 records in RAM.
INFO 2026-06-08 08:31:50 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,217
INFO 2026-06-08 08:31:50 MarkDuplicates Tracking 190008 as yet unmatched pairs. 57870 records in RAM.
INFO 2026-06-08 08:31:52 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,899
INFO 2026-06-08 08:31:52 MarkDuplicates Tracking 187182 as yet unmatched pairs. 55043 records in RAM.
INFO 2026-06-08 08:31:54 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,878
INFO 2026-06-08 08:31:54 MarkDuplicates Tracking 185455 as yet unmatched pairs. 53316 records in RAM.
INFO 2026-06-08 08:31:55 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 1s. Last read position: chr17:50,192,486
INFO 2026-06-08 08:31:55 MarkDuplicates Tracking 181720 as yet unmatched pairs. 49581 records in RAM.
INFO 2026-06-08 08:31:57 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 1s. Last read position: chr17:50,193,967
INFO 2026-06-08 08:31:57 MarkDuplicates Tracking 184506 as yet unmatched pairs. 52367 records in RAM.
INFO 2026-06-08 08:31:58 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,572
INFO 2026-06-08 08:31:58 MarkDuplicates Tracking 176806 as yet unmatched pairs. 44667 records in RAM.
INFO 2026-06-08 08:32:00 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,288
INFO 2026-06-08 08:32:00 MarkDuplicates Tracking 175896 as yet unmatched pairs. 43757 records in RAM.
INFO 2026-06-08 08:32:01 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,159
INFO 2026-06-08 08:32:01 MarkDuplicates Tracking 181433 as yet unmatched pairs. 49294 records in RAM.
INFO 2026-06-08 08:32:03 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,643
INFO 2026-06-08 08:32:03 MarkDuplicates Tracking 173238 as yet unmatched pairs. 41099 records in RAM.
INFO 2026-06-08 08:32:06 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 2s. Last read position: chr17:50,197,951
INFO 2026-06-08 08:32:06 MarkDuplicates Tracking 167042 as yet unmatched pairs. 34903 records in RAM.
INFO 2026-06-08 08:32:07 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 1s. Last read position: chr17:50,199,555
INFO 2026-06-08 08:32:07 MarkDuplicates Tracking 159170 as yet unmatched pairs. 27031 records in RAM.
INFO 2026-06-08 08:32:09 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 1s. Last read position: chr17:51,161,725
INFO 2026-06-08 08:32:09 MarkDuplicates Tracking 152962 as yet unmatched pairs. 20823 records in RAM.
INFO 2026-06-08 08:32:11 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 1s. Last read position: chr17:60,057,261
INFO 2026-06-08 08:32:11 MarkDuplicates Tracking 150179 as yet unmatched pairs. 18040 records in RAM.
INFO 2026-06-08 08:32:12 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 1s. Last read position: chr17:64,500,037
INFO 2026-06-08 08:32:12 MarkDuplicates Tracking 147858 as yet unmatched pairs. 15719 records in RAM.
INFO 2026-06-08 08:32:14 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 1s. Last read position: chr17:68,527,839
INFO 2026-06-08 08:32:14 MarkDuplicates Tracking 146577 as yet unmatched pairs. 14438 records in RAM.
INFO 2026-06-08 08:32:15 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 1s. Last read position: chr17:75,622,011
INFO 2026-06-08 08:32:15 MarkDuplicates Tracking 142418 as yet unmatched pairs. 10277 records in RAM.
INFO 2026-06-08 08:32:17 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 1s. Last read position: chr17:78,993,559
INFO 2026-06-08 08:32:17 MarkDuplicates Tracking 139628 as yet unmatched pairs. 7487 records in RAM.
INFO 2026-06-08 08:32:18 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 1s. Last read position: chr17:80,545,587
INFO 2026-06-08 08:32:18 MarkDuplicates Tracking 137126 as yet unmatched pairs. 4985 records in RAM.
INFO 2026-06-08 08:32:19 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 1s. Last read position: chr17:82,080,508
INFO 2026-06-08 08:32:19 MarkDuplicates Tracking 134230 as yet unmatched pairs. 2089 records in RAM.
INFO 2026-06-08 08:32:21 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 1s. Last read position: chr18:9,256,438
INFO 2026-06-08 08:32:21 MarkDuplicates Tracking 131252 as yet unmatched pairs. 6022 records in RAM.
INFO 2026-06-08 08:32:22 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 1s. Last read position: chr18:36,124,528
INFO 2026-06-08 08:32:22 MarkDuplicates Tracking 128994 as yet unmatched pairs. 3764 records in RAM.
INFO 2026-06-08 08:32:23 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 1s. Last read position: chr18:63,318,094
INFO 2026-06-08 08:32:23 MarkDuplicates Tracking 126672 as yet unmatched pairs. 1441 records in RAM.
INFO 2026-06-08 08:32:25 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 1s. Last read position: chr19:1,434,736
INFO 2026-06-08 08:32:25 MarkDuplicates Tracking 123370 as yet unmatched pairs. 49770 records in RAM.
INFO 2026-06-08 08:32:27 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 1s. Last read position: chr19:4,702,145
INFO 2026-06-08 08:32:27 MarkDuplicates Tracking 120208 as yet unmatched pairs. 46608 records in RAM.
INFO 2026-06-08 08:32:28 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 1s. Last read position: chr19:8,455,409
INFO 2026-06-08 08:32:28 MarkDuplicates Tracking 117053 as yet unmatched pairs. 43452 records in RAM.
INFO 2026-06-08 08:32:30 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 1s. Last read position: chr19:11,199,481
INFO 2026-06-08 08:32:30 MarkDuplicates Tracking 114097 as yet unmatched pairs. 40496 records in RAM.
INFO 2026-06-08 08:32:31 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 1s. Last read position: chr19:14,106,827
INFO 2026-06-08 08:32:31 MarkDuplicates Tracking 111354 as yet unmatched pairs. 37753 records in RAM.
INFO 2026-06-08 08:32:32 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 1s. Last read position: chr19:16,572,142
INFO 2026-06-08 08:32:32 MarkDuplicates Tracking 108476 as yet unmatched pairs. 34875 records in RAM.
INFO 2026-06-08 08:32:34 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 1s. Last read position: chr19:18,904,813
INFO 2026-06-08 08:32:34 MarkDuplicates Tracking 105376 as yet unmatched pairs. 31775 records in RAM.
INFO 2026-06-08 08:32:35 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 1s. Last read position: chr19:35,266,886
INFO 2026-06-08 08:32:35 MarkDuplicates Tracking 102715 as yet unmatched pairs. 29114 records in RAM.
INFO 2026-06-08 08:32:36 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 1s. Last read position: chr19:38,815,663
INFO 2026-06-08 08:32:36 MarkDuplicates Tracking 99400 as yet unmatched pairs. 25799 records in RAM.
INFO 2026-06-08 08:32:38 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:09:17s. Time for last 1,000,000: 1s. Last read position: chr19:39,928,199
INFO 2026-06-08 08:32:38 MarkDuplicates Tracking 96984 as yet unmatched pairs. 23383 records in RAM.
INFO 2026-06-08 08:32:39 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 1s. Last read position: chr19:41,894,208
INFO 2026-06-08 08:32:39 MarkDuplicates Tracking 93937 as yet unmatched pairs. 20334 records in RAM.
INFO 2026-06-08 08:32:40 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 1s. Last read position: chr19:44,907,793
INFO 2026-06-08 08:32:40 MarkDuplicates Tracking 91511 as yet unmatched pairs. 17907 records in RAM.
INFO 2026-06-08 08:32:42 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 1s. Last read position: chr19:46,787,492
INFO 2026-06-08 08:32:42 MarkDuplicates Tracking 87792 as yet unmatched pairs. 14188 records in RAM.
INFO 2026-06-08 08:32:44 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 1s. Last read position: chr19:49,107,638
INFO 2026-06-08 08:32:44 MarkDuplicates Tracking 85036 as yet unmatched pairs. 11432 records in RAM.
INFO 2026-06-08 08:32:45 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 1s. Last read position: chr19:50,309,698
INFO 2026-06-08 08:32:45 MarkDuplicates Tracking 81556 as yet unmatched pairs. 7951 records in RAM.
INFO 2026-06-08 08:32:46 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 1s. Last read position: chr19:54,587,261
INFO 2026-06-08 08:32:46 MarkDuplicates Tracking 79086 as yet unmatched pairs. 5481 records in RAM.
INFO 2026-06-08 08:32:48 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 1s. Last read position: chr19:57,620,861
INFO 2026-06-08 08:32:48 MarkDuplicates Tracking 75891 as yet unmatched pairs. 2286 records in RAM.
INFO 2026-06-08 08:32:49 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 1s. Last read position: chr20:417,839
INFO 2026-06-08 08:32:49 MarkDuplicates Tracking 73422 as yet unmatched pairs. 19014 records in RAM.
INFO 2026-06-08 08:32:50 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 1s. Last read position: chr20:11,922,766
INFO 2026-06-08 08:32:50 MarkDuplicates Tracking 70670 as yet unmatched pairs. 16262 records in RAM.
INFO 2026-06-08 08:32:52 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 1s. Last read position: chr20:31,684,381
INFO 2026-06-08 08:32:52 MarkDuplicates Tracking 68160 as yet unmatched pairs. 13752 records in RAM.
INFO 2026-06-08 08:32:54 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 1s. Last read position: chr20:36,185,286
INFO 2026-06-08 08:32:54 MarkDuplicates Tracking 65438 as yet unmatched pairs. 11030 records in RAM.
INFO 2026-06-08 08:32:55 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 1s. Last read position: chr20:45,025,111
INFO 2026-06-08 08:32:55 MarkDuplicates Tracking 62681 as yet unmatched pairs. 8271 records in RAM.
INFO 2026-06-08 08:32:57 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:09:36s. Time for last 1,000,000: 1s. Last read position: chr20:50,903,987
INFO 2026-06-08 08:32:57 MarkDuplicates Tracking 60256 as yet unmatched pairs. 5845 records in RAM.
INFO 2026-06-08 08:32:58 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 1s. Last read position: chr20:62,338,356
INFO 2026-06-08 08:32:58 MarkDuplicates Tracking 57263 as yet unmatched pairs. 2852 records in RAM.
INFO 2026-06-08 08:33:00 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 1s. Last read position: chr21:6,119,783
INFO 2026-06-08 08:33:00 MarkDuplicates Tracking 54316 as yet unmatched pairs. 10168 records in RAM.
INFO 2026-06-08 08:33:01 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,549
INFO 2026-06-08 08:33:01 MarkDuplicates Tracking 53049 as yet unmatched pairs. 8898 records in RAM.
INFO 2026-06-08 08:33:02 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 1s. Last read position: chr21:34,095,997
INFO 2026-06-08 08:33:02 MarkDuplicates Tracking 50625 as yet unmatched pairs. 6474 records in RAM.
INFO 2026-06-08 08:33:04 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 1s. Last read position: chr21:42,903,632
INFO 2026-06-08 08:33:04 MarkDuplicates Tracking 48028 as yet unmatched pairs. 3877 records in RAM.
INFO 2026-06-08 08:33:05 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 1s. Last read position: chr21:46,121,573
INFO 2026-06-08 08:33:05 MarkDuplicates Tracking 45467 as yet unmatched pairs. 1316 records in RAM.
INFO 2026-06-08 08:33:07 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 1s. Last read position: chr22:20,704,382
INFO 2026-06-08 08:33:07 MarkDuplicates Tracking 42412 as yet unmatched pairs. 18975 records in RAM.
INFO 2026-06-08 08:33:08 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 1s. Last read position: chr22:25,040,067
INFO 2026-06-08 08:33:08 MarkDuplicates Tracking 39420 as yet unmatched pairs. 15983 records in RAM.
INFO 2026-06-08 08:33:10 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 1s. Last read position: chr22:30,017,956
INFO 2026-06-08 08:33:10 MarkDuplicates Tracking 36633 as yet unmatched pairs. 13196 records in RAM.
INFO 2026-06-08 08:33:11 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 1s. Last read position: chr22:36,296,929
INFO 2026-06-08 08:33:11 MarkDuplicates Tracking 34011 as yet unmatched pairs. 10574 records in RAM.
INFO 2026-06-08 08:33:12 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 1s. Last read position: chr22:38,486,337
INFO 2026-06-08 08:33:12 MarkDuplicates Tracking 31237 as yet unmatched pairs. 7800 records in RAM.
INFO 2026-06-08 08:33:14 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 1s. Last read position: chr22:41,620,745
INFO 2026-06-08 08:33:14 MarkDuplicates Tracking 28373 as yet unmatched pairs. 4936 records in RAM.
INFO 2026-06-08 08:33:15 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 1s. Last read position: chr22:49,922,680
INFO 2026-06-08 08:33:15 MarkDuplicates Tracking 25483 as yet unmatched pairs. 2046 records in RAM.
INFO 2026-06-08 08:33:17 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 1s. Last read position: chrX:3,320,764
INFO 2026-06-08 08:33:17 MarkDuplicates Tracking 22646 as yet unmatched pairs. 19321 records in RAM.
INFO 2026-06-08 08:33:18 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: chrX:24,528,175
INFO 2026-06-08 08:33:18 MarkDuplicates Tracking 20053 as yet unmatched pairs. 16726 records in RAM.
INFO 2026-06-08 08:33:20 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 1s. Last read position: chrX:47,570,987
INFO 2026-06-08 08:33:20 MarkDuplicates Tracking 17640 as yet unmatched pairs. 14313 records in RAM.
INFO 2026-06-08 08:33:21 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 1s. Last read position: chrX:53,632,522
INFO 2026-06-08 08:33:21 MarkDuplicates Tracking 14898 as yet unmatched pairs. 11571 records in RAM.
INFO 2026-06-08 08:33:22 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 1s. Last read position: chrX:72,488,972
INFO 2026-06-08 08:33:22 MarkDuplicates Tracking 12150 as yet unmatched pairs. 8823 records in RAM.
INFO 2026-06-08 08:33:24 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 1s. Last read position: chrX:103,609,507
INFO 2026-06-08 08:33:24 MarkDuplicates Tracking 9962 as yet unmatched pairs. 6635 records in RAM.
INFO 2026-06-08 08:33:25 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chrX:132,069,494
INFO 2026-06-08 08:33:25 MarkDuplicates Tracking 7565 as yet unmatched pairs. 4238 records in RAM.
INFO 2026-06-08 08:33:27 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 1s. Last read position: chrX:154,360,020
INFO 2026-06-08 08:33:27 MarkDuplicates Tracking 5005 as yet unmatched pairs. 1677 records in RAM.
INFO 2026-06-08 08:33:28 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: GL000220.1:157,935
INFO 2026-06-08 08:33:28 MarkDuplicates Tracking 2458 as yet unmatched pairs. 39 records in RAM.
INFO 2026-06-08 08:33:29 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 1s. Last read position: KI270733.1:178,749
INFO 2026-06-08 08:33:29 MarkDuplicates Tracking 62 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 08:33:29 MarkDuplicates Read 328066460 records. 0 pairs never matched.
INFO 2026-06-08 08:33:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 29537351784; totalMemory: 42177921024; maxMemory: 63585648640
INFO 2026-06-08 08:33:52 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:33:59 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:34:12 OpticalDuplicateFinder Large duplicate set. size = 1468
INFO 2026-06-08 08:34:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,660
INFO 2026-06-08 08:34:17 OpticalDuplicateFinder Large duplicate set. size = 1351
INFO 2026-06-08 08:34:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,850
INFO 2026-06-08 08:34:31 OpticalDuplicateFinder Large duplicate set. size = 1088
INFO 2026-06-08 08:34:31 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,291
INFO 2026-06-08 08:34:31 OpticalDuplicateFinder Large duplicate set. size = 1243
INFO 2026-06-08 08:34:31 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,010
INFO 2026-06-08 08:34:32 OpticalDuplicateFinder Large duplicate set. size = 1034
INFO 2026-06-08 08:34:32 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,694
INFO 2026-06-08 08:34:32 OpticalDuplicateFinder Large duplicate set. size = 1201
INFO 2026-06-08 08:34:32 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,489
INFO 2026-06-08 08:34:32 OpticalDuplicateFinder Large duplicate set. size = 1026
INFO 2026-06-08 08:34:32 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,148
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder Large duplicate set. size = 1384
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,946
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder Large duplicate set. size = 1102
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,612
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder Large duplicate set. size = 1037
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,187
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder Large duplicate set. size = 1182
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,381
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder Large duplicate set. size = 1065
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,669
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder Large duplicate set. size = 1286
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,835
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder Large duplicate set. size = 2126
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,837
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,850
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder Large duplicate set. size = 1217
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,671
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder Large duplicate set. size = 1410
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,729
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder Large duplicate set. size = 1200
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,303
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder Large duplicate set. size = 1367
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,250
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder Large duplicate set. size = 1205
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,494
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder Large duplicate set. size = 1151
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,154
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder Large duplicate set. size = 1251
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,261
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder Large duplicate set. size = 1427
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,286
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder Large duplicate set. size = 1039
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,909
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder Large duplicate set. size = 1190
INFO 2026-06-08 08:34:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,831
INFO 2026-06-08 08:34:38 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:34:38 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:35:12 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:35:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300666800; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 08:35:21 MarkDuplicates Marking 239308859 records as duplicates.
INFO 2026-06-08 08:35:21 MarkDuplicates Found 4950737 optical duplicate clusters.
INFO 2026-06-08 08:35:21 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:35:37 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:15s. Time for last 10,000,000: 15s. Last read position: chr1:109,095,727
INFO 2026-06-08 08:35:51 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:29s. Time for last 10,000,000: 14s. Last read position: chr1:156,050,308
INFO 2026-06-08 08:36:07 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:45s. Time for last 10,000,000: 15s. Last read position: chr1:228,106,798
INFO 2026-06-08 08:36:22 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:00s. Time for last 10,000,000: 14s. Last read position: chr2:87,795,744
INFO 2026-06-08 08:36:37 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:15s. Time for last 10,000,000: 15s. Last read position: chr2:178,696,108
INFO 2026-06-08 08:36:52 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:30s. Time for last 10,000,000: 15s. Last read position: chr2:215,409,564
INFO 2026-06-08 08:37:07 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:45s. Time for last 10,000,000: 15s. Last read position: chr3:49,531,814
INFO 2026-06-08 08:37:22 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:00s. Time for last 10,000,000: 15s. Last read position: chr3:195,867,976
INFO 2026-06-08 08:37:37 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:15s. Time for last 10,000,000: 14s. Last read position: chr5:34,023,919
INFO 2026-06-08 08:37:52 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:30s. Time for last 10,000,000: 15s. Last read position: chr5:150,117,650
INFO 2026-06-08 08:38:07 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:02:45s. Time for last 10,000,000: 14s. Last read position: chr6:31,992,211
INFO 2026-06-08 08:38:23 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:01s. Time for last 10,000,000: 15s. Last read position: chr7:5,345,748
INFO 2026-06-08 08:38:38 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:16s. Time for last 10,000,000: 15s. Last read position: chr7:102,553,291
INFO 2026-06-08 08:38:54 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:32s. Time for last 10,000,000: 15s. Last read position: chr8:100,721,396
INFO 2026-06-08 08:39:09 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:03:47s. Time for last 10,000,000: 15s. Last read position: chr9:99,035,368
INFO 2026-06-08 08:39:24 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:02s. Time for last 10,000,000: 15s. Last read position: chr10:69,015,814
INFO 2026-06-08 08:39:39 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:17s. Time for last 10,000,000: 15s. Last read position: chr11:47,175,084
INFO 2026-06-08 08:39:54 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:32s. Time for last 10,000,000: 14s. Last read position: chr11:78,079,658
INFO 2026-06-08 08:40:09 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:04:47s. Time for last 10,000,000: 14s. Last read position: chr12:40,499,697
INFO 2026-06-08 08:40:25 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:03s. Time for last 10,000,000: 16s. Last read position: chr12:106,977,896
INFO 2026-06-08 08:40:40 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:18s. Time for last 10,000,000: 14s. Last read position: chr14:35,308,079
INFO 2026-06-08 08:40:55 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:05:33s. Time for last 10,000,000: 15s. Last read position: chr15:43,793,755
INFO 2026-06-08 08:41:09 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:05:48s. Time for last 10,000,000: 14s. Last read position: chr16:14,627,305
INFO 2026-06-08 08:41:24 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:03s. Time for last 10,000,000: 15s. Last read position: chr16:32,174,324
INFO 2026-06-08 08:41:40 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:18s. Time for last 10,000,000: 15s. Last read position: chr17:37,538,355
INFO 2026-06-08 08:41:55 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:06:33s. Time for last 10,000,000: 15s. Last read position: chr17:50,188,560
INFO 2026-06-08 08:42:11 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:06:49s. Time for last 10,000,000: 15s. Last read position: chr17:50,197,951
INFO 2026-06-08 08:42:26 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:04s. Time for last 10,000,000: 15s. Last read position: chr18:9,256,438
INFO 2026-06-08 08:42:41 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:20s. Time for last 10,000,000: 15s. Last read position: chr19:35,266,886
INFO 2026-06-08 08:42:57 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:07:35s. Time for last 10,000,000: 15s. Last read position: chr20:417,839
INFO 2026-06-08 08:43:12 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:07:50s. Time for last 10,000,000: 15s. Last read position: chr21:42,903,632
INFO 2026-06-08 08:43:27 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:05s. Time for last 10,000,000: 15s. Last read position: chrX:24,528,175
INFO 2026-06-08 08:43:44 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:08:23s. Time for last 10,000,000: 17s. Last read position: */*
INFO 2026-06-08 08:43:45 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:43:45 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:43:45 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:43:45 MarkDuplicates Before output close freeMemory: 201378984; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:43:45 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:43:45 MarkDuplicates After output close freeMemory: 104134992; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:43:45 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 20.44 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory